Package ubic.gemma.core.loader.genome

Interface FastaCmd

All Known Implementing Classes:

SimpleFastaCmd

public interface FastaCmd

Interface representing a class that can retrieve sequences from Blast databases. (In later versions of BLAST this is known as Blastdbcmd)

Author:

pavlidis

Method Summary

Modifier and Type	Method	Description
Collection<BioSequence>	getBatchAccessions(Collection<String> accessions, String database)
Collection<BioSequence>	getBatchAccessions(Collection<String> accessions, String database, String blastHome)
Collection<BioSequence>	getBatchIdentifiers(Collection<Integer> identifiers, String database)
Collection<BioSequence>	getBatchIdentifiers(Collection<Integer> identifiers, String database, String blastHome)
BioSequence	getByAccession(String accession, String database)
BioSequence	getByAccession(String accession, String database, String blastHome)
BioSequence	getByIdentifier(int identifier, String database)
BioSequence	getByIdentifier(int identifier, String database, String blastHome)

Method Detail

getByAccession

BioSequence getByAccession(String accession,
                           String database)

getByIdentifier

BioSequence getByIdentifier(int identifier,
                            String database)

getBatchAccessions

Collection<BioSequence> getBatchAccessions(Collection<String> accessions,
                                           String database)

getBatchIdentifiers

Collection<BioSequence> getBatchIdentifiers(Collection<Integer> identifiers,
                                            String database)

getByAccession

BioSequence getByAccession(String accession,
                           String database,
                           String blastHome)

getByIdentifier

BioSequence getByIdentifier(int identifier,
                            String database,
                            String blastHome)

getBatchAccessions

Collection<BioSequence> getBatchAccessions(Collection<String> accessions,
                                           String database,
                                           String blastHome)

getBatchIdentifiers

Collection<BioSequence> getBatchIdentifiers(Collection<Integer> identifiers,
                                            String database,
                                            String blastHome)